I tried contacting partner support, and have not received any response, and this issue affect many merchants using my apps, I am getting desperate here.
I am pretty sure this issue can be replicated in all Shopify stores, the replication steps are as follow :
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Send a HTTP POST request to the REST Admin API for Creating Checkout, and in the request, include custom items (variant_id: null, custom: true)
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Then in the response returned, copy the “web_url”
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Access the “web_url” using web browser, you will notice the custom item is gone.
Shopify Development / API Team, please look into this, this started happening since 2-3 weeks ago